Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in arabidopsis

Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprograming as reflected by differential expression of ~20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 (RRC1), previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants

A pragmatic Bayesian approach to predictive uncertainty

We describe an approach to regression based on building a probabilistic model with the aid of visualization. The “stereopsis” data set in the predictive uncertainty challenge is used as a case study, for which we constructed a mixture of neural network experts model. We describe both the ideal Bayesian approach and computational shortcuts required to obtain timely results

A Deep Dive into Docker Hub’s Security Landscape - A story of inheritance?

Abstract. This Chapter presents the PASCAL 1 Evaluating Predictive Uncertainty Challenge, introduces the contributed Chapters by the participants who obtained outstanding results, and provides a discussion with some lessons to be learnt. The Challenge was set up to evaluate the ability of Machine Learning algorithms to provide good “probabilistic predictions”, rather than just the usual “point predictions ” with no measure of uncertainty, in regression and classification problems. Participants had to compete on a number of regression and classification tasks, and were evaluated by both traditional losses that only take into account point predictions and losses we proposed that evaluate the quality of the probabilistic predictions.

An Analysis of Inference with the Universum

We study a pattern classification algorithm which has recently been proposed by Vapnik and coworkers. It builds on a new inductive principle which assumes that in addition to positive and negative data, a third class of data is available, termed the Universum. We assay the behavior of the algorithm by establishing links with Fisher discriminant analysis and oriented PCA, as well as with an SVM in a projected subspace (or, equivalently, with a data-dependent reduced kernel). We also provide experimental results